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Merged
LouisLeNezet merged 1 commit into from
Jun 30, 2026
+78 −94
Merged

Update to topic maxquant #12203

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12 changes: 1 addition & 11 deletions modules/nf-core/maxquant/lfq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ process MAXQUANT_LFQ {

output:
tuple val(meta), path("${prefix}/*.txt"), emit: maxquant_txt
path "versions.yml" , emit: versions
tuple val("${task.process}"), val("maxquant"), eval("maxquant --version 2>&1 | sed 's/MaxQuantCmd //' || true"), emit: versions_maxquant, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -29,11 +29,6 @@ process MAXQUANT_LFQ {
${args} \\
mqpar_changed.xml
mv combined/txt/*.txt ${prefix}/

cat <<-END_VERSIONS > versions.yml
"${task.process}":
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
END_VERSIONS
"""

stub:
Expand All @@ -54,10 +49,5 @@ process MAXQUANT_LFQ {
touch ${prefix}/peptides.txt
touch ${prefix}/proteinGroups.txt
touch ${prefix}/summary.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
END_VERSIONS
"""
}
40 changes: 29 additions & 11 deletions modules/nf-core/maxquant/lfq/meta.yml
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@@ -1,17 +1,19 @@
name: maxquant_lfq
description: Run standard proteomics data analysis with MaxQuant, mostly dedicated
to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
description: Run standard proteomics data analysis with MaxQuant, mostly
dedicated to label-free. Paths to fasta and raw files needs to be marked by
"PLACEHOLDER"
keywords:
- sort
- proteomics
- mass-spectroscopy
tools:
- maxquant:
description: MaxQuant is a quantitative proteomics software package designed for
analyzing large mass-spectrometric data sets. License restricted.
description: MaxQuant is a quantitative proteomics software package designed
for analyzing large mass-spectrometric data sets. License restricted.
homepage: https://www.maxquant.org/
documentation: http://coxdocs.org/doku.php?id=maxquant:start
licence: ["http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"]
licence:
- "http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"
identifier: biotools:maxquant
input:
- - meta:
Expand Down Expand Up @@ -45,13 +47,29 @@ output:
description: tables with peptides and protein information
pattern: "*.{txt}"
ontologies: []
versions_maxquant:
- - ${task.process}:
type: string
description: The name of the process
- maxquant:
type: string
description: The name of the tool
- maxquant --version 2>&1 | sed 's/MaxQuantCmd //' || true:
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software version
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- maxquant:
type: string
description: The name of the tool
- maxquant --version 2>&1 | sed 's/MaxQuantCmd //' || true:
type: eval
description: The expression to obtain the version of the tool

authors:
- "@veitveit"
maintainers:
Expand Down
18 changes: 5 additions & 13 deletions modules/nf-core/maxquant/lfq/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists:true),
file(params.modules_testdata_base_path + 'proteomics/parameter/mqpar.xml', checkIfExists:true)
]
input[1] = Channel.of([
input[1] = channel.of([
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_12.raw'),
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_14.raw')
]).collect()
Expand All @@ -29,18 +29,13 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot( // Need to check only the file names as empty files are created
process.out.maxquant_txt.collect{
it[1].collect{ file(it).getName() }
},
process.out.versions,
).match() }
// Need to check only the file names as empty files are created
{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["maxquant_txt"])).match() }
)
}
}

test("yeast_UPS - msspectra raw -- stub") {
tag "stub"
options "-stub"
when {
process {
Expand All @@ -50,7 +45,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists:true),
file(params.modules_testdata_base_path + 'proteomics/parameter/mqpar.xml', checkIfExists:true)
]
input[1] = Channel.of([
input[1] = channel.of([
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_12.raw'),
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_14.raw')
]).collect()
Expand All @@ -60,10 +55,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
102 changes: 43 additions & 59 deletions modules/nf-core/maxquant/lfq/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"yeast_UPS - msspectra raw -- stub": {
"content": [
{
"0": [
"maxquant_txt": [
[
{
"id": "test"
Expand All @@ -25,76 +25,60 @@
]
]
],
"1": [
"versions.yml:md5,60dc5d20588a3b49c7d0c453bd98c5ee"
],
"versions_maxquant": [
[
"MAXQUANT_LFQ",
"maxquant",
"2.0.3.0"
]
]
}
],
"timestamp": "2026-06-30T15:43:06.639002941",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
},
"yeast_UPS - msspectra raw": {
"content": [
{
"maxquant_txt": [
[
{
"id": "test"
},
[
"Oxidation (M)Sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"allPeptides.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"evidence.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"matchedFeatures.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"modificationSpecificPeptides.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"ms3Scans.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"msScans.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"msms.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"msmsScans.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"mzRange.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"parameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"peptides.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"proteinGroups.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
"Oxidation (M)Sites.txt",
"allPeptides.txt",
"evidence.txt",
"matchedFeatures.txt",
"modificationSpecificPeptides.txt",
"ms3Scans.txt",
"msScans.txt",
"msms.txt",
"msmsScans.txt",
"mzRange.txt",
"parameters.txt",
"peptides.txt",
"proteinGroups.txt",
"summary.txt"
]
]
],
"versions": [
"versions.yml:md5,60dc5d20588a3b49c7d0c453bd98c5ee"
"versions_maxquant": [
[
"MAXQUANT_LFQ",
"maxquant",
"2.0.3.0"
]
]
},
{
"MAXQUANT_LFQ": {
"maxquant": "2.0.3.0"
}
}
],
"timestamp": "2026-06-30T16:12:14.910445538",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-05-07T17:41:13.129192804"
},
"yeast_UPS - msspectra raw": {
"content": [
[
[
"Oxidation (M)Sites.txt",
"allPeptides.txt",
"evidence.txt",
"matchedFeatures.txt",
"modificationSpecificPeptides.txt",
"ms3Scans.txt",
"msScans.txt",
"msms.txt",
"msmsScans.txt",
"mzRange.txt",
"parameters.txt",
"peptides.txt",
"proteinGroups.txt",
"summary.txt"
]
],
[
"versions.yml:md5,60dc5d20588a3b49c7d0c453bd98c5ee"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-05-07T17:40:29.652923118"
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
}
}
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